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Core commits
RSS
Recent Commits to bioperl-live:master Clarify the POD a bit Doc example Typos Merge branch 'master' of github.com:bioperl/bioperl-live Create a unique using the percent Merge pull request #32 from fschwach/master make _coord_adjust work with negative positions updated POD Merge pull request #31 from fschwach/master corrected passing of opts_ref in 'ligate' changed _new_seq_via_clone to using Bio::Root::Root::clone (in turn uses Clone or Storable if available) instead of Clone::Fast to avoid extra dependency implmeneted clone_obj option to clone rather than call new to creat the product molecules. Using Clone::Fast for cloning objects. Added feature for deletion sites and bugfixes changed behaviour of feature ends in deletions: a deletion no longer corrected call to 'ligate' method with named parameters corrected call to revcom_with_features in "ligate" and corrected POD for method "ligate" modified existing methods _coord_revcom and _coord_adjust to make use of the new methods _single_loc_object_from_collection and _location_objects_from_coordinate_list to reduce code-duplication added tests for delete/insert/ligate methods hanged recursive acquisition of sub features for deletion/insertion from using remove_SeqFeatures to get_SeqFeatures. The former has the side-effect of modifying the original sequence object, which should be avoided Added POD for new features

Run commits
RSS
Recent Commits to bioperl-run:master Merge pull request #4 from markjohnson/mark_johnson-email-update Updated my email address. Add missing arguments and a test Change location of working dir, not sure what is correct here Change location of tempdir, not sure what is correct here Module and tests for Raxml Add messages to *t Remove unused code Remove code related to MPI Typo Remove ID lines Add no_memory_check Add program_name param Minimal documentation Correct number New module and test for FastTree Remove code related to MPI, definitely the wrong place for it Modify program_name() for MPI version, not sure all args are set correctly yet. Modify program_name() for MPI version, not sure all args are set correctly yet. Modify program_name() for MPI version, not sure all args are set correctly yet.

Ext commits
RSS
Recent Commits to bioperl-ext:master moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet use UPPPER_TOL to catch the case when the expectation maximization step fixed Vitebi typo Fixed the typemap and also a memory bug in viterbi function in HMM.xs adding FEEDBACK:Support section to pod Bump to 1.007 (similar to trunk) ext patches (courtesy Thomas Jahns) get rid of some unended comment warnings from C compiler -fPIC needed for lib construction include errno definition removed DEBUG=1 IUPAC DNA support IUPAC DNA test case Add some helper code and tests to demo evalue oddities (bug 1857); casting issue? Add cast to correct pointer type (get rid of warnings) update version to last bioperl release bug 2329 bug 2074/2329 Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this? bug 2074

Bioperl-DB (BioSQL)
RSS
Recent Commits to bioperl-db:master updates since last release update skipped files add MANIFEST.SKIP buzgilla -> redmine [RT 44466] remove corba-related scripts, now obsolete squash perl 5.12 warning ignore conf file add minimal .gitignore file weird duplication removed committing patch for bug #2958 test commit to check SVN::Notify Build.PL now checks for DBD drivers and attempts to DTRT remove MANIFEST.SKIP update Changes fix empty POD section some pod cleaning main trunk version is wrong * 02species.t now compared to similarly behaving instance, also creates comparable array [bug 2092] moved Bio into lib to make Module::Build installation more normal